Instead of the notion that humans are the dominant environmental force on Earth, bio-scientist Predrag B. Slijepčević has another story to tell — one that puts microbes at the center. In his book, “Biocivilisations: A New Look at the Science of Life,” Slijepčević writes that as organisms with far greater evolutionary experience than us, microbes, fungi, plants and other animals can teach us valuable lessons. Life, after all, existed without humans for more than 99.99% of the Earth’s existence. Take humans out of the equation, and the biosphere’s natural trajectory would continue. But take microbes out, and the whole thing would collapse. “It is a constant reminder that humans are non-essential by-products of what mostly amounts to microbial evolutionary games,” Slijepčević writes. He notes that microbes, for their part, are virtually everywhere — deep in the oceans, high on mountain peaks, amongst tropospheric clouds, in every kind of forest and even in our bodies. In this excerpt from chapter one of “Biocivilisations,” Slijepčević describes the basic elements of microbial biocivilization – language, mind and memory – and shows how almost all elements of human civilization have precursors in the bacterial world.

Predrag B. Slijepčević is a senior lecturer in the Department of Life Sciences at Brunel University London. He is a bio-scientist interested in the philosophy of biology and has published widely in peer-reviewed journals. In particular, Slijepčević investigates how biological systems, from bacteria to animals and beyond, perceive and process environmental stimuli (that is, biological information) and how this processing, which is a form of natural learning, affects the organism–environment interactions. “Biocivilisations,” his first book, is a 2024 Nautilus Book Award Gold Medal Winner: Restorative Earth Practices.

Microbial Language

Ever since life emerged on Earth, there has been constant communication amongst organisms. But this communication is deceptive. These are no talking heads, but the communication is not unlike our language. Instead, organisms communicate through exchanging biological signals and semiotic signs – chemical messages, electrical impulses, scents, body movements, etc.

Bacteria were the first organisms to speak up. Unfortunately, we are deaf to their conversations. Bacteria ‘talk’ to each other, and to all other organisms on the planet. For example, bacteria from our microbiome – the collection of bacteria, viruses, archaea and fungi inside and on the surface of our bodies – talk to us behind our backs. They bypass the conscious part of our intellect and talk to the unconscious. Scientists have discovered ‘conversations’ between bacteria living in our guts and cells in our brains. This type of talk is called the gut-brain axis. Bacteria from our guts direct our brain cells to secrete serotonin, which improves mood.²¹ Gut bacteria drug our nervous systems without us even being aware that it’s happening.

Bacteria from our microbiome – the collection of bacteria, viruses, archaea and fungi inside and on the surface of our bodies – talk to us behind our backs. They bypass the conscious part of our intellect and talk to the unconscious.

Language is a set of symbols that convey meaning. Every linguistic sign reflects the superiority of mind over matter. When we utter a word, we launch a non-material abstraction full of meaning into the semiotic stratosphere. There, our symbols mix with bacterial, viral, plant and animal symbols in true Tower of Babel fashion, with the crucial difference that the number of languages in the semiotic stratosphere is far greater than in the biblical story. This fascinating biosemiotic construction intrigued the celebrated writer Umberto Eco, who was once impressed by the thought of a biosemiotician friend: ‘instead of thinking whether cells speak like us, the question should be asked whether we speak like cells’.²²

How do bacteria talk to each other? James Shapiro discovered their semiotic symbols – i.e. the ‘words’ of bacterial language. He identified a large group of chemicals that bacteria exchange in communication with each other.²³ There are linguistic chemicals used in the communication of bacteria of the same species. There are also linguistic chemicals exchanged between bacteria of different species, in the manner of constructed international languages such as Esperanto or the true global language, English.

The most successful communicators, including cross-kingdom communicators, are bacteria – true biological polyglots.

Conversations between bacteria and people, or bacteria and plants, are conducted in a language that scientists call cross-kingdom communication. The most successful communicators, including cross-kingdom communicators, are bacteria – true biological polyglots. Bacteria speak and understand all the languages of the world, from their own mother tongues, to plant and animal languages, to cross-kingdom communication that reverberates with the biosphere in the most complex music the universe has ever known. Bacteria also talk to viruses, semi-living biogenic structures, by detecting the words of a viral language – only recently discovered – based on arbitrium, which consists of a peptide composed of six amino acids.²⁴ Thus, mostly thanks to bacteria, the biosphere becomes the semiosphere – a compendium of biological signs and the domination of mind over matter.

The Microbial Mind

We know from experience that words don’t make sense without the mind to decode and interpret them. The mind unites spoken words into sentences, then into stories, or perhaps into algorithms (if words are replaced by mathematical symbols). Without the mind, there is no storytelling, and this is also true of the biosphere and the Gaian mind. In other words, if bacteria have no mind, their talk is pointless; it represents little more than a form of mindless chatter. Mainstream biology, in a true Cartesian manner, does not allow for the existence of a bacterial mind. Even when leading scientists are willing to get into details of bacterial language, the idea of a bacterial mind controlling bacterial language is considered off-limits.²⁵

Non-conventional scientists such as Eshel Ben-Jacob, Gregory Bateson and Lynn Margulis, however, have argued against the short-sightedness of mainstream biology, and especially against the prejudices that scientists cultivate towards non-human organisms – a kind of evolution-based anthropic racism rooted in modern culture. Ben-Jacob developed the concept of the ‘bacterial brain’, which is complete only when combined with Bateson’s concept of the natural mind. 

Ben-Jacob argued, similarly to Shapiro, that bacteria are multicellular communities (or colonies), with a typical colony consisting of 10⁹-10¹² individual organisms, and with the entire bacterial population connected into a global bacterial superorganism or bacteriosphere. Bacterial colonies are constantly using language to solve the problems presented by their environments. A colony will assess a problem – for example, food shortages – through the collective examination of the environment and collective gathering of information using bacterial language. Once the nature of the problem is determined, bacterial colonies use information about past problems, stored in the colony’s collective memory. In this manner, the colony begins distributed information processing to solve the emerging problem. The problem-solving process transforms the colony into a structure most similar to the human brain. Bacterial colonies become ‘super-brains’ that perform acts of natural computation.²⁶ When we look from this perspective at the planetary bacteriosphere, in which bacterial colonies are connected through bacterial language – a living equivalent of the internet – we see glimpses of a planetwide bacterial brain that has maintained biogeochemical balance for billions of years.

When we look from this perspective at the planetary bacteriosphere, in which bacterial colonies are connected through bacterial language – a living equivalent of the internet – we see glimpses of a planetwide bacterial brain that has maintained biogeochemical balance for billions of years.

Gregory Bateson would probably agree that a bacterial colony constitutes a form of the natural mind. Bateson often reminded his audience that the mind exists in nature in many more places than just inside our heads. To assess whether a biogenic structure meets the requirements of the natural mind, Bateson applied six criteria²⁷ :

1. The mind is the unity of the parts that communicate with each other;
2. The mental process creates feedback;
3. Communication between parts is driven by the ‘difference that makes a difference’ or biological information;
4. The mental process requires energy;
5. Biological information directs changes in the physical environment;
6. Biological hierarchy is constrained by both bottom-up (cells to ecosystem) and top-down (ecosystem to cells) forces.

Bacterial colonies and the planetary bacteriosphere meet all of Bateson’s criteria of the natural mind. More than a century prior, Darwin stated the following about the mind: ‘The difference in mind between man and the higher animals, great as it is, certainly is one of degree and not of kind.’²⁸ Bateson, however, was much more radical. For Bateson: ‘Mind is the essence of being alive.’ Interestingly, Bateson considered Lamarck to be the greatest biologist in history, not Darwin. Presumably because, amongst other things, Lamarck sensed the intelligence of bacteria.

Microbial Memory

The collective memory of microbes goes back almost four billion years to the moment when these tiny and invisible organisms emerged on Earth. How is this possible? The first line of memory is the microbial genome that stores blueprints for the oldest protein constructs. This is no exaggeration but simply a consequence of the biological postulate of vertical gene transfer. Since bacteria and archaea were the first organisms in the history of life, all organisms that evolved from them, including humans, share their four-billion-year genetic heritage.²⁹ 

The first line of memory is the microbial genome that stores blueprints for the oldest protein constructs.

But genes are only one line of memory. The other line of memory is much more important: the organism as a biological construct that incorporates genes. Genes are important, but they are secondary. The emblem of neo-Darwinism – ‘the selfish gene’ – is becoming an obsolete concept. How can a gene be selfish when it lacks a self? This is a question Lynn Margulis asked Richard Dawkins at a meeting. No one has yet come up with a convincing answer.

Margulis argued that the basic unit of life, and therefore of memory, can only be the simplest cell – a microbe such as a bacterium or an archaeon. Each bacterium is an open thermodynamic system that exchanges matter, energy and information with its environment. Each bacterium has an instinctive sense of its own body in the context of the external environment. It has perception, memory and the ability to make decisions, plan the future and communicate. These characteristics are to be expected from a biological system that has a sense of its own body.

A gene or a piece of a DNA molecule, on the other hand, is a simple biological code that serves the bacterium as an aid in the transmission of biological information, and in the process exchanges matter and energy with the environment. This code is meaningless without the context of the bacterial ‘body’ as an open thermodynamic system. The DNA code is a form of bacterial ‘thought’ – a hypothesis subjected to an evolutionary test.

Interestingly, the source of genes, which are biological ‘thought’ material, is not only bacterial or archaeal genomes, but viruses, plasmids, naked genes and other DNA pieces involved in horizontal gene transfer (HGT). Some scientists argue that viruses may be a precursor to life – a position supported by the fact that bacteria, the most dominant form of life in the biosphere, cannot exist without viruses.³⁰ The bacteriosphere needs an auxiliary biogenic structure. Scientists call this structure the virosphere. The virosphere and the bacteriosphere are the foundations of life. The most numerous viruses in the virosphere are those that infect bacteria (although bacteria developed a system of defence against unwanted viruses, or, metaphorically, unwanted ‘thoughts’, so that they can preserve their own ‘common sense’).³¹

Genetically stored information only serves to trigger more complex collective information-processing abilities, which then create new knowledge that bacteria need to learn about new conditions in the environment. Thanks to this memory, the bacterial colony turns into a brain-like entity capable of natural learning, and thus becomes a form of Bateson’s natural mind.

Eshel Ben-Jacob defines the nature of bacterial memory as follows: a combination of (a) internally stored information in the genome of each bacterium and (b) information that the bacterial society, which makes up the colony, collects from its environment and stores in the structure of the colony. In other words, genetic memory by itself is not enough for the process of wiring bacteria to the environment. Genetically stored information only serves to trigger more complex collective information-processing abilities, which then create new knowledge that bacteria need to learn about new conditions in the environment. Thanks to this memory, the bacterial colony turns into a brain-like entity capable of natural learning, and thus becomes a form of Bateson’s natural mind. The conclusion is self-evident: the ability of bacterial colonies to remember past events transforms the planetary bacteriosphere into the collective memory of the biosphere.

No matter how much Homo sapiens might deny the dominance of microbes on Earth, and artificially impose human dominance, reality refutes us. The Covid-19 pandemic is one example amongst many that ruthlessly revealed the holes in our understanding of biological reality. The bacteriosphere and virosphere are the basis of life (see Chapter 2). Although we can’t deny the usefulness of the term in revealing the destructiveness of human impact, the Anthropocene is little more than an anti-Copernican delusion of modern civilisation.

The above excerpt is from Predrag B. Slijepčević’s book “Biocivilisations: A New Look at the Science of Life” (Chelsea Green Publishing, May 2023) and is printed with permission from the publisher.

^21. Ohad Lewin-Epstein, Ranit Aharonov and Lilach Hadany, ‘Microbes can help explain the evolution of host altruism,’ Nature Communications 8 (2017), https://doi.org/10.1038/ncomms14040.

^22. Kalevi Kull, ‘Umberto Eco on the biosemiotics of Giorgio Prodi,’ Sign Systems Studies 46 (2018): 352–364.

^23. Details of bacterial communication, known as quorum sensing, can be found in these papers: James A. Shapiro, ‘Thinking about bacterial populations as multicellular organisms,’ Annual Review of Microbiology 52 (1889): 81–104; James A. Shapiro, ‘Bacteria as multicellular organisms’, Scientific American June (1988): 82–89.

^24. Zohar Erez et al., ‘Communication between viruses guides lysis-lysogeny decisions,’ Nature 541 (2017): 488–493.

^25. Interpreting bacterial communication without a coordinating activity of mind, as an emergent phenomenon in a social group, is reflected in the term ‘small talk’, used to describe bacterial language in the following paper: Bonnie L. Bassler, ‘Small talk: Cell-to-cell communication in bacteria,’ Cell 109 (2002): 421–424.

^26. Ben-Jacob, ‘Bacterial wisdom, Gödel’s theorem,’ Physica A.

^27. Gregory Bateson, Mind and Nature: A Necessary Unity (New York: E. P. Dutton, 1979), 92.

^28. Charles Darwin, Descent of Man: Selection in Relation to Sex (New York: D. Appleton and Company, 1889), 126.

^29. This is the consequence of vertical gene transfer or the evolutionary tree of life.

^30. Laura A. Hug et al., ‘A new view of the tree of life,’ Nature Microbiology 1 (2016), https://doi.org/10.1038/nmicrobiol.2016.48.

^31. Karin Moelling and Felix Broecker, ‘Viruses and evolution – viruses first? A personal perspective,’ Frontiers in Microbiology 10 (2019), https://doi.org/10.3389/fmicb.2019.00523.